Figures for Shiny

Figures AMU rapport sectoriel bovins laitiers

Créer les figures interactives demande aussi un certain temps de logiciel. Nous allons donc les créer et les sauvegarder dans un format interactif (.rds) et nous pourrons ainsi appeller les figures directement dans l’interface Shiny sans avoir à les créer dans l’interface. Ce sera plus rapide comme rendu ET l’interface Shiny sera simplifiée.

#Open the datasets

max <- read.csv("data/max.csv")
min <- read.csv("data/min.csv")

min$Year <- factor(min$Year)
max$Year <- factor(max$Year)
max$Route <- factor(max$Route)

#Rename Route
max$Route <- ifelse(max$Route=="IM_L", "IMM-Lactation",
                    ifelse(max$Route=="IM_T", "IMM-Tarissement",
                           ifelse(max$Route=="INJ", "Injectable", 
                                  ifelse(max$Route=="IU", "IU", 
                                         ifelse(max$Route=="ORAL", "PO", "Topique")))))

Figure utilisation globale par année

AMU totale

DCD

library(dplyr)

## 
## Attachement du package : 'dplyr'

## Les objets suivants sont masqués depuis 'package:stats':
## 
##     filter, lag

## Les objets suivants sont masqués depuis 'package:base':
## 
##     intersect, setdiff, setequal, union

library(plotly)

## Le chargement a nécessité le package : ggplot2

## 
## Attachement du package : 'plotly'

## L'objet suivant est masqué depuis 'package:ggplot2':
## 
##     last_plot

## L'objet suivant est masqué depuis 'package:stats':
## 
##     filter

## L'objet suivant est masqué depuis 'package:graphics':
## 
##     layout

library(htmlwidgets)

fig <- min %>%
  plot_ly(
    y = ~total_DCD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation totale', 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 900),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )

saveWidget(fig, "Figures/Total AMU DCD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Total AMU DCD.rds")

#e <- readRDS("Figures/Total AMU DCD.rds")
#e

DDD

fig <- min %>%
  plot_ly(
    y = ~total_DDD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation totale', 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 900),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Total AMU DDD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Total AMU DDD.rds")

#e <- readRDS("Figures/Total AMU DDD.rds")
#e

AMU catégorie I

DCD

fig <- min %>%
  plot_ly(
    y = ~cat1_DCD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie I', 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 500),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat1 AMU DCD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie I en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat1 AMU DCD.rds")

#e <- readRDS("Figures/Cat1 AMU DCD.rds")
#e

DDD

fig <- min %>%
  plot_ly(
    y = ~cat1_DDD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie I', 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 700),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat1 AMU DDD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie 1 en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat1 AMU DDD.rds")

#e <- readRDS("Figures/Cat1 AMU DDD.rds")
#e

AMU catégorie II

DCD

fig <- min %>%
  plot_ly(
    y = ~cat2_DCD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie II', 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 500),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat2 AMU DCD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie II en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat2 AMU DCD.rds")

#e <- readRDS("Figures/Cat2 AMU DCD.rds")
#e

DDD

fig <- min %>%
  plot_ly(
    y = ~cat2_DDD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie II', 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 500),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat2 AMU DDD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie II en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat2 AMU DDD.rds")

#e <- readRDS("Figures/Cat2 AMU DDD.rds")
#e

AMU catégorie III

DCD

fig <- min %>%
  plot_ly(
    y = ~cat3_DCD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie III', 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 500),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat3 AMU DCD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie III en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat3 AMU DCD.rds")

#e <- readRDS("Figures/Cat3 AMU DCD.rds")
#e

DDD

fig <- min %>%
  plot_ly(
    y = ~cat3_DDD,
    split = ~Year,
    type = 'violin',
    box = list(
      visible = T
    ),
    meanline = list(
      visible = T
    ),
    spanmode="hard"
  ) 

fig <- fig %>%
  layout(title = 'Utilisation des antibiotiques de catégorie III', 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.0f',  
                      #range = list(0, 500),
                      zeroline = TRUE), 
         showlegend = FALSE
         
  )
saveWidget(fig, "Figures/Cat3 AMU DDD.html", selfcontained = F, libdir = "lib")
fig

Taux d’utilisation des antibiotiques de catégorie III en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat3 AMU DDD.rds")

#e <- readRDS("Figures/Cat3 AMU DDD.rds")
#e

Figure AMU par voie d’administration

AMU totale

DCD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~total_DCD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation totale par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 530)), 
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Total AMU Route DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques par voie d’administration en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Total AMU Route DCD.rds")

#d <- readRDS("Figures/Total AMU Route DCD.rds")
#d

DDD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~total_DDD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation totale par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 1500)), 
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

  saveWidget(fig, "Figures/Total AMU Route DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques par voie d’administration en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Total AMU Route DDD.rds")

#d <- readRDS("Figures/Total AMU Route DDD.rds")
#d

AMU catégorie I

DCD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat1_DCD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie I par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 200)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Cat1 AMU Route DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 1 par voie d’administration en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat1 AMU Route DCD.rds")

#d <- readRDS("Figures/Cat1 AMU Route DCD.rds")
#d

DDD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat1_DDD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie I par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 350)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Cat1 AMU Route DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 1 par voie d’administration en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat1 AMU Route DDD.rds")

#d <- readRDS("Figures/Cat1 AMU Route DDD.rds")
#d

AMU catégorie II

DCD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat2_DCD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie II par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 450)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Cat2 AMU Route DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 2 par voie d’administration en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat2 AMU Route DCD.rds")

#d <- readRDS("Figures/Cat2 AMU Route DCD.rds")
#d

DDD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat2_DDD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie II par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 1500)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))
saveWidget(fig, "Figures/Cat2 AMU Route DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 2 par voie d’administration en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat2 AMU Route DDD.rds")

#d <- readRDS("Figures/Cat2 AMU Route DDD.rds")
#d

AMU catégorie 3

DCD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat3_DCD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie III par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 250)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Cat3 AMU Route DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 3 par voie d’administration en DCD.

#plotly_build()
#saveRDS(fig, "Figures/Cat3 AMU Route DCD.rds")

#d <- readRDS("Figures/Cat3 AMU Route DCD.rds")
#d

DDD

fig <- plot_ly(max, 
                         x = ~Route, 
                         y = ~cat3_DDD, 
                         color = ~Year, 
                         type = "box",
                         marker=list(color="white"))%>% 
  layout(boxmode="group",
         title = "Utilisation des antibiotiques de catégorie III par voie d'administration", 
         yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                      hoverformat = '.1f',  
                      range = list(0, 1300)),
         xaxis = list(title = "Voie d'administration"),
         legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h"))

saveWidget(fig, "Figures/Cat3 AMU Route DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

Taux d’utilisation des antibiotiques de catégorie 3 par voie d’administration en DDD.

#plotly_build()
#saveRDS(fig, "Figures/Cat3 AMU Route DDD.rds")

#d <- readRDS("Figures/Cat3 AMU Route DDD.rds")
#d

AMU par famille d’antibiotique

Catégorie 1

DCD

#I don't know why but "Year" is always showing up in the bottom part of the figure, even with xaxis=list(title="Année")

min$Année <- factor(min$Year)

#Categorie 1
library(plotly)
fig <- plot_ly(min,
               x = ~Année,
               y = ~TGCeph_DCD, 
               type = 'box', 
               name="Céphalosporines de 3e génération",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Fluoro_DCD,
                         type = 'box', 
                         name="Fluoroquinolones",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Poly_DCD,
                         type = 'box', 
                         name="Polymyxines",
                         marker=list(color="white")
                         )

fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie I par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 170)),
                     legend= list(x = 0.1, 
                      y = 0.95, 
                      orientation="h")
         )

saveWidget(fig, "Figures/cat1_fam_DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat1_fam_DCD.rds")

#d <- readRDS("Figures/cat1_fam_DCD.rds")
#d

DDD

#Categorie 1
library(plotly)
fig <- plot_ly(min,
               x = ~Année,
               y = ~TGCeph_DDD, 
               type = 'box', 
               name="Céphalosporines de 3e génération",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Fluoro_DDD,
                         type = 'box', 
                         name="Fluoroquinolones",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Poly_DDD,
                         type = 'box', 
                         name="Polymyxines",
                         marker=list(color="white")
                         )

fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie I par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 350)),
                     legend= list(x = 0.1, 
                      y = 0.95, 
                      orientation="h")
         )
saveWidget(fig, "Figures/cat1_fam_DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat1_fam_DDD.rds")

#d <- readRDS("Figures/cat1_fam_DDD.rds")
#d

Catégorie II

DCD

#Categorie 2

fig <- plot_ly(min,
               x = ~Année,
               y = ~BLSensPen_DCD, 
               type = 'box', 
               name="Pen. sens. aux beta-lact.",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Amin_DCD,
                         type = 'box', 
                         name="Aminoglycosides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~FGCeph_DCD,
                         type = 'box', 
                         name="1ère gén. céphapirines",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Linco_DCD,
                         type = 'box', 
                         name="Lincosamides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~BLResPen_DCD,
                         type = 'box', 
                         name="Pen. résist. aux beta-lact.",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~TMS_DCD,
                         type = 'box', 
                         name="Trimethoprim-sulfonamides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Macr_DCD,
                         type = 'box', 
                         name="Macrolides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~PenES_DCD,
                         type = 'box', 
                         name="Pen. à spectre étendu",
                         marker=list(color="white")
                         )

fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie II par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 275)),
                     legend= list(x = 100, 
                      y = 0.95, 
                      orientation="h")
         )
saveWidget(fig, "Figures/cat2_fam_DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat2_fam_DCD.rds")

#d <- readRDS("Figures/cat2_fam_DCD.rds")
#d

DDD

#Categorie 2

fig <- plot_ly(min,
               x = ~Année,
               y = ~BLSensPen_DDD, 
               type = 'box', 
               name="Pen. sens. aux beta-lact.",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Amin_DDD,
                         type = 'box', 
                         name="Aminoglycosides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~FGCeph_DDD,
                         type = 'box', 
                         name="1ère gén. céphapirines",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Linco_DDD,
                         type = 'box', 
                         name="Lincosamides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~BLResPen_DDD,
                         type = 'box', 
                         name="Pen. résist. aux beta-lact.",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~TMS_DDD,
                         type = 'box', 
                         name="Trimethoprim-sulfonamides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Macr_DDD,
                         type = 'box', 
                         name="Macrolides",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~PenES_DDD,
                         type = 'box', 
                         name="Pen. à spectre étendu",
                         marker=list(color="white")
                         )

fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie II par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 1300)),
                     legend= list(x = 100, 
                      y = 0.95, 
                      orientation="h")
         )
saveWidget(fig, "Figures/cat2_fam_DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat2_fam_DDD.rds")

#d <- readRDS("Figures/cat2_fam_DDD.rds")
#d

Catégorie III

DCD

#Categorie 3
fig <- plot_ly(min,
               x = ~Année,
               y = ~Tetr_DCD, 
               name = 'Tétracyclines',
               type = 'box', 
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Sulf_DCD,
                         name="Sulfonamides",
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Amph_DCD, 
                         name = 'Amphénicols',
                         type = 'box', 
                         marker=list(color="white")
                         )


fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie III par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 100)) ,
                     legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h")
         )
saveWidget(fig, "Figures/cat3_fam_DCD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat3_fam_DCD.rds")

#d <- readRDS("Figures/cat3_fam_DCD.rds")
#d

DDD

#Categorie 3
fig <- plot_ly(min,
               x = ~Année,
               y = ~Tetr_DDD, 
               name = 'Tétracyclines',
               type = 'box', 
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Sulf_DDD,
                         name="Sulfonamides",
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Année,
                         y = ~Amph_DDD, 
                         name = 'Amphénicols',
                         type = 'box', 
                         marker=list(color="white")
                         )


fig<- fig %>%
              layout(boxmode="group",
                     title = "Utilisation des antibiotiques de catégorie III par famille d'antibiotiques", 
                     yaxis = list(title = "Taux d'utilisation (Dose-jour/100 animaux-année)",
                     hoverformat = '.1f',  
                     range = list(0, 300)),
                     legend= list(x = 0.2, 
                      y = 0.95, 
                      orientation="h")
         )
saveWidget(fig, "Figures/cat3_fam_DDD.html", selfcontained = F, libdir = "lib")

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

fig

## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'

#plotly_build()
#saveRDS(fig, "Figures/cat3_fam_DDD.rds")

#d <- readRDS("Figures/cat3_fam_DDD.rds")
#d

Write table with summary stats

Nous allons calculer les médianes qui pourraient être “appellées” dans le texte de l’interface. Ça évitera de les modifier à la pièce. Au besoin, on pourrait ajouter d’autres mesures tels Q1, Q3, moyenne, etc que l’on voudrait mentionner dans le texte.

#Write table with all medians summary stats

sum_stats <- min %>% 
  group_by(Year) %>% 
  summarize(med_total_DCD=round(quantile(total_DCD, 0.50)),
            med_total_DDD=round(quantile(total_DDD, 0.50)),
            
            med_cat1_DCD=round(quantile(cat1_DCD, 0.50)),
            med_cat1_DDD=round(quantile(cat1_DDD, 0.50)),
            med_cat2_DCD=round(quantile(cat2_DCD, 0.50)),
            med_cat2_DDD=round(quantile(cat2_DDD, 0.50)),
            med_cat3_DCD=round(quantile(cat3_DCD, 0.50)),
            med_cat3_DDD=round(quantile(cat3_DDD, 0.50)),
            
            med_PenES_DCD=round(quantile(PenES_DCD, 0.50)),
            med_PenES_DDD=round(quantile(PenES_DDD, 0.50)),  
            
            med_BLResPen_DCD=round(quantile(BLResPen_DCD, 0.50)),
            med_BLResPen_DDD=round(quantile(BLResPen_DDD, 0.50)), 
            
            med_BLSensPen_DCD=round(quantile(BLSensPen_DCD, 0.50)),
            med_BLSensPen_DDD=round(quantile(BLSensPen_DDD, 0.50)),
            
            med_FGCeph_DCD=round(quantile(FGCeph_DCD, 0.50)),
            med_FGCeph_DDD=round(quantile(FGCeph_DDD, 0.50)), 
            
            med_TGCeph_DCD=round(quantile(TGCeph_DCD, 0.50)),
            med_TGCeph_DDD=round(quantile(TGCeph_DDD, 0.50)),
            
            med_Fluoro_DCD=round(quantile(Fluoro_DCD, 0.50)),
            med_Fluoro_DDD=round(quantile(Fluoro_DDD, 0.50)), 
            
            med_Amph_DCD=round(quantile(Amph_DCD, 0.50)),
            med_Amph_DDD=round(quantile(Amph_DDD, 0.50)),  
            
            med_Macr_DCD=round(quantile(Macr_DCD, 0.50)),
            med_Macr_DDD=round(quantile(Macr_DDD, 0.50)),  
            
            med_Tetr_DCD=round(quantile(Tetr_DCD, 0.50)),
            med_Tetr_DDD=round(quantile(Tetr_DDD, 0.50)), 
            
            med_Amin_DCD=round(quantile(Amin_DCD, 0.50)),
            med_Amin_DDD=round(quantile(Amin_DDD, 0.50)),  
            
            med_Sulf_DCD=round(quantile(Sulf_DCD, 0.50)),
            med_Sulf_DDD=round(quantile(Sulf_DDD, 0.50)), 
            
            med_Linco_DCD=round(quantile(Linco_DCD, 0.50)),
            med_Linco_DDD=round(quantile(Linco_DDD, 0.50)), 
            
            med_Poly_DCD=round(quantile(Poly_DCD, 0.50)),
            med_Poly_DDD=round(quantile(Poly_DDD, 0.50)), 
            
            med_TMS_DCD=round(quantile(TMS_DCD, 0.50)),
            med_TMS_DDD=round(quantile(TMS_DDD, 0.50))
            )
write.csv(sum_stats,"data/stats.csv", row.names = FALSE)

sum_stats_route <- max %>% 
  group_by(Route, Year) %>% 
  summarize(med_total_DCD=round(quantile(total_DCD, 0.50)),
            med_total_DDD=round(quantile(total_DDD, 0.50)),
           
            med_cat1_DCD=round(quantile(cat1_DCD, 0.50)),
            med_cat1_DDD=round(quantile(cat1_DDD, 0.50)),
            med_cat2_DCD=round(quantile(cat2_DCD, 0.50)),
            med_cat2_DDD=round(quantile(cat2_DDD, 0.50)),
            med_cat3_DCD=round(quantile(cat3_DCD, 0.50)),
            med_cat3_DDD=round(quantile(cat3_DDD, 0.50)),
            
            med_PenES_DCD=round(quantile(PenES_DCD, 0.50)),
            med_PenES_DDD=round(quantile(PenES_DDD, 0.50)),  
            
            med_BLResPen_DCD=round(quantile(BLResPen_DCD, 0.50)),
            med_BLResPen_DDD=round(quantile(BLResPen_DDD, 0.50)), 
            
            med_BLSensPen_DCD=round(quantile(BLSensPen_DCD, 0.50)),
            med_BLSensPen_DDD=round(quantile(BLSensPen_DDD, 0.50)),
            
            med_FGCeph_DCD=round(quantile(FGCeph_DCD, 0.50)),
            med_FGCeph_DDD=round(quantile(FGCeph_DDD, 0.50)), 
            
            med_TGCeph_DCD=round(quantile(TGCeph_DCD, 0.50)),
            med_TGCeph_DDD=round(quantile(TGCeph_DDD, 0.50)),
            
            med_Fluoro_DCD=round(quantile(Fluoro_DCD, 0.50)),
            med_Fluoro_DDD=round(quantile(Fluoro_DDD, 0.50)), 
            
            med_Amph_DCD=round(quantile(Amph_DCD, 0.50)),
            med_Amph_DDD=round(quantile(Amph_DDD, 0.50)),  
            
            med_Macr_DCD=round(quantile(Macr_DCD, 0.50)),
            med_Macr_DDD=round(quantile(Macr_DDD, 0.50)),  
            
            med_Tetr_DCD=round(quantile(Tetr_DCD, 0.50)),
            med_Tetr_DDD=round(quantile(Tetr_DDD, 0.50)), 
            
            med_Amin_DCD=round(quantile(Amin_DCD, 0.50)),
            med_Amin_DDD=round(quantile(Amin_DDD, 0.50)),  
            
            med_Sulf_DCD=round(quantile(Sulf_DCD, 0.50)),
            med_Sulf_DDD=round(quantile(Sulf_DDD, 0.50)), 
            
            med_Linco_DCD=round(quantile(Linco_DCD, 0.50)),
            med_Linco_DDD=round(quantile(Linco_DDD, 0.50)), 
            
            med_Poly_DCD=round(quantile(Poly_DCD, 0.50)),
            med_Poly_DDD=round(quantile(Poly_DDD, 0.50)), 
            
            med_TMS_DCD=round(quantile(TMS_DCD, 0.50)),
            med_TMS_DDD=round(quantile(TMS_DDD, 0.50))
            )

## `summarise()` has grouped output by 'Route'. You can override using the
## `.groups` argument.

write.csv(sum_stats_route,"data/stats_route.csv", row.names = FALSE)